Hello Chris, Are you refining individual atomic B factors or grouped? Perhaps the B factors of the terminal atoms of the side chain are being restrained to too low of a B factor resulting in excessive negative density?
Scott On Apr 4, 2012, at 8:16 AM, Chris Meier wrote: > Dear all, > I am refining the X-ray structure of a protein: > Data to ~2A were collected at a latest-generation synchrotron. > The 2fo-Fc maps are crisp, the model of the protein is complete and I am > reasonably happy with the stats (R below 20%, Rfree below 25% in Refmac 5.5). > However, I am seeing a lot of negative difference density, > especially around sulphur atoms (negative density around -9 sigma) > and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with > negative density around -6 sigma). > Has anyone observed this before? > I have found CCP4bb postings discussing radiation damange of suplphur atoms > (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). > Can this also happen with oxygen atoms? > What would be an appropriate way to deal with this issue during refinement? > Suggestions greatly appreciated. > Thanks, > Chris >
